Displaying 20 results from an estimated 100000 matches similar to: "how to make gwaa.data"
2010 Nov 03
0
how to handle 'gwaa@gtdata' ?
I have a few questions about GenABEL, gwaa data.
1) is there a universal way that most GenABEL people use to add more
individuals into a 'gwaa' data? For example, I have a 'gwaa' data, but I
need to add some dummy parents, for 'gwaa at phdata', it's easy to add these
rows, but for 'gwaa at gtdata', I think I need to create SNP data as '0 0 0 0
0.....'
2010 Feb 23
1
GenABEL - problems with load.gwaa.data
Hi all! I am using GenABEL on R for GWAS analysis. I am having a couple of
issues:
First, I am having a problem reading files (.map, & .ped, size 900Mb, using
windows 32-bit) onto R in the "convert.snp.ped" statement. I am thinking
this problem is likely due to the large size of the files & my version of R
is not able to handle them, since I can read in smaller files.
2009 Sep 08
0
Fred Hutchinson Cancer Research Center - Systems Analyst/Programmer III/IV (AD-22564)
Systems Analyst /Programmer III/IV (AD-22564)
About Us
Fred Hutchinson Cancer Research Center, home of three Nobel laureates,
is an independent, nonprofit research institution dedicated to the
development and advancement of biomedical research to eliminate cancer
and other potentially fatal diseases. Recognized internationally for its
pioneering work in bone-marrow transplantation, the
2011 Nov 24
0
loop through columns in S4 objects
Dear experts,
I am trying to perform an association using snpStats.
I have a snp matrix called 'plink' which contains my genotype data (as
a list of $genotypes, $map, $fam), and a phenotype data frame which
contains the outcomes (outcome1, outcome2,...) I would like to
associate with the genotype.
My question is, how do I loop through the outcomes? This type of data
seems different from
2012 Aug 24
0
A question about GRAMMAR calculations in the FAM_MDR algorithm
Dear R developers:
I am a PHD candidate student in the school of public health of Peking
University and my major is genetic epidemiology. I am learning the FAM-MDR
algorithm, which is used to detect the gene-gene and gene-environment
interactions in the data of pedigree. The codes were written by Tom
Cattaert of the University of Liege. The algorithms and the sample datasets
are available at
2011 Jun 21
4
Re; Getting SNPS from PLINK to R
I a using plink on a large SNP dataset with a .map and .ped file.
I want to get some sort of file say a list of all the SNPs that plink is
saying that I have. ANyideas on how to do this?
--
Thanks,
Jim.
[[alternative HTML version deleted]]
2011 Jun 21
1
Getting SNPS from PLINK to R
snpMatrix package is quite nice (read.plink())
2008 Dec 24
0
command Polygenic gives error message concerning dimensions of data
Dear Sir/Madam,
Since a few day now I try to use the command "polygenic" from the GenAbel
package. However, I keep bumping up against an error message: "Error in
polygenic(Testo, kin = kinship, data = data1) : dimension of outcome and
kinship.matrix do not match".
My data exists of 1240 individuals with 74 markers. It mainly consists of
small families (2 or more brothers,
2011 Jun 28
1
means and error bars on xyplot for binary data
Hi,
I have binary (0,1) data for a trait as my response variable, and
a dependent variable, genotype, with three classes (AA, AB, BB).
I would like to plot this data so that across the three genoytpes, even
though the points are all either 0 or 1, i want them to stack up or be seen
using 'jitter'. So far I have been able to do this using xyplot {lattice}
(code below) but could not get
2008 Jul 25
1
Plink bed files
Hi All,
does anyone know how to import binary .bed files generated by Plink (http://pngu.mgh.harvard.edu/~purcell/plink/
) into R? the Plink FAQ explains how to conver other types of files,
not the .bed.
Cheers,
Federico
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 75941602 Fax
2011 Apr 14
1
integer and floating-point storage
I note that "current implementations of R use 32-bit integers for integer
vectors," but I am working with large arrays that contain integers from 0
to 3, so they could be stored as unsigned 8-bit integers. Can R do this?
(FYI -- This is for storing minor-allele counts for genetic studies.
There are 0, 1 or 2 minor alleles and 3 would represent missing.)
It is theoretically possible
2013 Jul 02
2
Recoding variables based on reference values in data frame
I'm new to R (previously used SAS primarily) and I have a genetics data
frame consisting of genotypes for each of 300+ subjects (ID1, ID2, ID3,
...) at 3000+ genetic locations (SNP1, SNP2, SNP3...). A small subset of
the data is shown below:
SNP_ID SNP1 SNP2 SNP3 SNP4 Maj_Allele C G C A Min_Allele T A T G ID1
CC GG CT AA ID2 CC GG CC AA ID3 CC GG
nc
AA
2013 Nov 08
1
SNPRelate: Plink conversion
Hi,
Following my earlier posts about having problems performing a PCA, I have
worked out what the problem is. The problem lies within the PLINK to gds
conversion.
It seems as though the SNPs are imported as "samples" and in turn, the
samples are recognised as SNPs:
>snpsgdsSummary("chr2L")
Some values of snp.position are invalid (should be > 0)!
Some values of
2002 Nov 27
0
R genetics package now available
The "genetics" package for handling single-locus genetic data is now
available on CRAN in both source and Windows binary formats. The purpose of
this package is to make it easy to create and manipulate genetic
information, and to facility use of this information in statistical models.
The library includes classes and methods for creating, representing, and
manipulating genotypes
2002 Nov 27
0
R genetics package now available
The "genetics" package for handling single-locus genetic data is now
available on CRAN in both source and Windows binary formats. The purpose of
this package is to make it easy to create and manipulate genetic
information, and to facility use of this information in statistical models.
The library includes classes and methods for creating, representing, and
manipulating genotypes
2013 Feb 28
2
data grouping and fitting mixed model with lme function
Dear all,
I have data from the following experimental design and trying to fit a mixed model with lme function according to following steps but struggling. Any help is deeply appreciated.
1) Experimental design: I have 40 plants each of which has 4 clones. Each clone planted to one of 4 blocks. Phenotypes were collected from each clone for 3 consecutive years. I have genotypes of plants. I
2012 Dec 13
0
GLMM - lme4 - binomial family, quadrinomial data: Can one partition be response and another be dependent variable?
Hi there. At first glance it sounded to me as an obvious "no-no" question.
But, for some reason, I ran some trials and results looked pretty
intriguing.
So, I checked 14 genotypes (8 plants from each randomly chosen in the
field) on 4 different dates and measured them under 2 different
temperatures. As a response, I have 4 different partition of how light is
absorbed in the leaf and
2006 Apr 21
2
forcing apply() to return data frame
Hi All,
I am (almost) successfully using apply() to apply a function recursively
on a data matrix. The function is question is as.genotype() from the
library 'genetics'
apply(subset(chr1, names$breed == 'lab'),2,as.genotype,sep ="")
Unfortuantely apply puts it's results into a matrix object rather than a
data frame, tranforming my factors into numerics and
2007 Sep 05
0
New R package plink for separate calibration IRT linking
The first version of the package plink has been uploaded to CRAN.
plink is a package for conducting unidimensional IRT scaling and chain
linking for multiple groups for single-format or mixed-format common
items. The package supports eight IRT models and four calibration
methods.
Dichotomous Models:
1PL, 2PL, 3PL
Polytomous Models:
-Graded response model
-Partial credit model
-Generalized
2007 Sep 05
0
New R package plink for separate calibration IRT linking
The first version of the package plink has been uploaded to CRAN.
plink is a package for conducting unidimensional IRT scaling and chain
linking for multiple groups for single-format or mixed-format common
items. The package supports eight IRT models and four calibration
methods.
Dichotomous Models:
1PL, 2PL, 3PL
Polytomous Models:
-Graded response model
-Partial credit model
-Generalized